LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-747-g3fabe8e766-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# SPC/E water with hybrid mc/md via fix hmc, using its rigid option

units           real
boundary        p p p
atom_style      full

read_data       data.hmc.spce
Reading data file ...
  orthogonal box = (-1.2 -1.2 -1.2) to (1.2 1.2 1.2)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (-1.2 -1.2 -1.2) to (1.2 1.2 1.2)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  2 bonds
  reading angles ...
  1 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.004 seconds
replicate       4 4 4
Replication is creating a 4x4x4 = 64 times larger system...
  orthogonal box = (-1.2 -1.2 -1.2) to (8.4 8.4 8.4)
  1 by 1 by 1 MPI processor grid
  192 atoms
  128 bonds
  64 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  replicate CPU = 0.002 seconds

mass            1 15.9994
mass            2 1.00784

neighbor        2.0 bin
neigh_modify    every 1 delay 0 check yes

pair_style      lj/cut/coul/long 9.0
pair_modify     tail yes mix arithmetic
kspace_style    pppm 1.0e-5

pair_coeff      1 1 0.1554015 3.166
pair_coeff      2 2 0 0

bond_style      harmonic
bond_coeff      1 554.1349 1.000

angle_style     harmonic
angle_coeff     1 45.7696 109.47

timestep        1.0

thermo          100
#dump            1 all atom 10 dump.hmc_rigid

fix             1 all rigid/small molecule
Fix rigid/small setup ...
  create bodies CPU = 0.000 seconds
  64 rigid bodies with 192 atoms
  0.95789707 = max distance from body owner to body atom

# equilibrate a bit
run             1000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.3592552
  grid = 12 12 12
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0015096129
  estimated relative force accuracy = 4.5461544e-06
  using double precision FFTW3
  3d grid and FFT values/proc = 6859 1728
Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 11
  ghost atom cutoff = 11
  binsize = 5.5, bins = 2 2 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 15.35 | 15.35 | 15.35 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              2848.4633      151.27379      2999.737       1031168.6    
       100   5.861911e-07   2848.4634      151.27379      2999.7372      1031168.7    
       200   2669.3811      1838.5388      151.27379      3000.3412      894607.86    
       300   3851.5999      1389.8324      151.27379      2999.1789      761433.46    
       400   3784.368       1416.4051      151.27379      3000.3001      766552.76    
       500   4152.4074      1277.6852      151.27379      3000.9062      716423.17    
       600   3979.7474      1344.2593      151.27379      3002.1177      745256.48    
       700   4131.3642      1287.199       151.27379      3002.4539      714615.97    
       800   3963.1546      1351.831       151.27379      3003.408       733572.42    
       900   4128.2848      1290.0822      151.27379      3004.1713      718849.31    
      1000   4154.3135      1281.1884      151.27379      3005.1311      718771.27    
Loop time of 3.86826 on 1 procs for 1000 steps with 192 atoms

Performance: 22.336 ns/day, 1.075 hours/ns, 258.514 timesteps/s, 49.635 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.1427     | 2.1427     | 2.1427     |   0.0 | 55.39
Bond    | 0.0054541  | 0.0054541  | 0.0054541  |   0.0 |  0.14
Kspace  | 0.59682    | 0.59682    | 0.59682    |   0.0 | 15.43
Neigh   | 0.63029    | 0.63029    | 0.63029    |   0.0 | 16.29
Comm    | 0.11852    | 0.11852    | 0.11852    |   0.0 |  3.06
Output  | 0.00028424 | 0.00028424 | 0.00028424 |   0.0 |  0.01
Modify  | 0.37053    | 0.37053    | 0.37053    |   0.0 |  9.58
Other   |            | 0.003692   |            |       |  0.10

Nlocal:            192 ave         192 max         192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6715 ave        6715 max        6715 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         115822 ave      115822 max      115822 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 115822
Ave neighs/atom = 603.23958
Ave special neighs/atom = 2
Neighbor list builds = 122
Dangerous builds = 0

# start HMC run

timestep        3.0  # large timestep
fix             2 all hmc 200 654123 300.0 rigid 1

thermo_style    custom step temp pe ke etotal f_2 f_2[*]

run             5000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.3592552
  grid = 12 12 12
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0015096129
  estimated relative force accuracy = 4.5461544e-06
  using double precision FFTW3
  3d grid and FFT values/proc = 6859 1728
Generated 1 of 1 mixed pair_coeff terms from arithmetic mixing rule
Per MPI rank memory allocation (min/avg/max) = 18.48 | 18.48 | 18.48 Mbytes
   Step          Temp          PotEng         KinEng         TotEng          f_2           f_2[1]         f_2[2]         f_2[3]         f_2[4]         f_2[5]    
      1000   295.23964      1432.4622      111.76677      1544.2289      0              0              0              0              0              0            
      1100   1744.7613      873.29257      660.50184      1533.7944      0              0              0              0              0              0            
      1200   1865.8643      829.64972      706.34694      1535.9967      1              1              1             -602.81246      594.58017     -8.2322859    
      1300   1737.6765      884.45503      657.8198       1542.2748      1              1              1             -602.81246      594.58017     -8.2322859    
      1400   280.71451      829.64972      106.26809      935.91781      0.5            1              2             -28.977506      40.354047      11.376542    
      1500   936.85156      575.34009      354.65722      929.99731      0.5            1              2             -28.977506      40.354047      11.376542    
      1600   1061.8149      527.11863      401.9637       929.08234      0.66666667     2              3             -302.53109      295.69561     -6.8354766    
      1700   989.04241      556.87391      374.41474      931.28866      0.66666667     2              3             -302.53109      295.69561     -6.8354766    
      1800   305.97484      527.11863      115.83071      642.94935      0.5            2              4              11.801879     -10.170557      1.6313212    
      1900   591.6152       415.9006       223.96355      639.86415      0.5            2              4              11.801879     -10.170557      1.6313212    
      2000   585.26241      419.06278      221.55862      640.6214       0.6            3              5             -108.05585      105.72791     -2.3279469    
      2100   695.86831      375.65868      263.42991      639.08859      0.6            3              5             -108.05585      105.72791     -2.3279469    
      2200   317.85229      419.06278      120.32708      539.38986      0.5            3              6             -6.4579305      6.8401743      0.38224382   
      2300   494.51535      350.56333      187.20515      537.76849      0.5            3              6             -6.4579305      6.8401743      0.38224382   
      2400   561.97537      324.59524      212.74301      537.33825      0.57142857     4              7             -94.467543      92.415934     -2.0516086    
      2500   514.86598      342.32947      194.90915      537.23862      0.57142857     4              7             -94.467543      92.415934     -2.0516086    
      2600   301.38261      324.59524      114.09227      438.68751      0.5            4              8              38.27272      -37.753499      0.51922104   
      2700   423.23724      277.20742      160.22191      437.42933      0.5            4              8              38.27272      -37.753499      0.51922104   
      2800   364.64348      300.43295      138.04048      438.47343      0.55555556     5              9             -24.162289      23.948215     -0.21407479   
      2900   387.15834      291.97544      146.56377      438.53922      0.55555556     5              9             -24.162289      23.948215     -0.21407479   
      3000   407.56736      283.33646      154.28987      437.62633      0.6            6              10            -17.096486      16.249388     -0.84709759   
      3100   369.27126      298.99854      139.79239      438.79093      0.6            6              10            -17.096486      16.249388     -0.84709759   
      3200   415.97374      280.73434      157.47222      438.20656      0.63636364     7              11            -2.6021185      3.1823444      0.58022598   
      3300   384.12266      293.34102      145.41458      438.7556       0.63636364     7              11            -2.6021185      3.1823444      0.58022598   
      3400   436.79613      273.0659       165.3548       438.4207       0.66666667     8              12            -7.6684488      7.8825836      0.21413477   
      3500   405.36789      285.08723      153.45724      438.54447      0.66666667     8              12            -7.6684488      7.8825836      0.21413477   
      3600   325.31146      273.0659       123.15084      396.21674      0.61538462     8              13             1.3005023     -0.81167631     0.488826     
      3700   332.23744      270.11923      125.77276      395.89199      0.61538462     8              13             1.3005023     -0.81167631     0.488826     
      3800   354.44162      261.45917      134.17844      395.63761      0.64285714     9              14            -11.606725      11.027597     -0.57912787   
      3900   338.90311      267.80703      128.29614      396.10316      0.64285714     9              14            -11.606725      11.027597     -0.57912787   
      4000   327.20972      272.23945      123.86945      396.1089       0.66666667     10             15             10.780279     -10.308989      0.47129051   
      4100   348.64025      264.03668      131.98226      396.01894      0.66666667     10             15             10.780279     -10.308989      0.47129051   
      4200   404.43833      242.85063      153.10534      395.95596      0.6875         11             16            -29.388824      29.235885     -0.15293818   
      4300   451.97226      224.43836      171.09992      395.53828      0.6875         11             16            -29.388824      29.235885     -0.15293818   
      4400   464.0666       219.97947      175.67839      395.65786      0.70588235     12             17            -22.871155      22.57305      -0.29810469   
      4500   434.5519       231.5422       164.50522      396.04742      0.70588235     12             17            -22.871155      22.57305      -0.29810469   
      4600   444.67517      227.64923      168.33751      395.98674      0.72222222     13             18             7.6697557     -7.3408762      0.32887949   
      4700   401.50364      244.50875      151.99437      396.50312      0.72222222     13             18             7.6697557     -7.3408762      0.32887949   
      4800   465.44589      219.60618      176.20053      395.80672      0.73684211     14             19            -8.0430445      7.8630224     -0.18002213   
      4900   400.19835      245.03734      151.50024      396.53757      0.73684211     14             19            -8.0430445      7.8630224     -0.18002213   
      5000   432.35901      232.51322      163.67507      396.1883       0.75           15             20             12.907042     -12.525462      0.38158022   
      5100   507.735        204.1419       192.20962      396.35152      0.75           15             20             12.907042     -12.525462      0.38158022   
      5200   280.79969      232.51322      106.30034      338.81356      0.71428571     15             21            -27.000021      27.616467      0.61644506   
      5300   387.11293      191.83568      146.54659      338.38227      0.71428571     15             21            -27.000021      27.616467      0.61644506   
      5400   369.37714      198.733        139.83247      338.56547      0.72727273     16             22            -33.780227      33.532133     -0.24809399   
      5500   401.61069      186.39101      152.0349       338.42591      0.72727273     16             22            -33.780227      33.532133     -0.24809399   
      5600   391.5761       190.03819      148.23618      338.27437      0.73913043     17             23            -8.6948028      8.4037037     -0.29109913   
      5700   417.75659      180.37941      158.14713      338.52654      0.73913043     17             23            -8.6948028      8.4037037     -0.29109913   
      5800   408.2949       183.51819      154.56529      338.08348      0.75           18             24            -6.5200073      6.3291156     -0.19089166   
      5900   404.54301      185.70636      153.14497      338.85132      0.75           18             24            -6.5200073      6.3291156     -0.19089166   
      6000   389.86246      190.89744      147.58746      338.4849       0.76           19             25             7.3792569     -6.9778359      0.401421     
Loop time of 20.0542 on 1 procs for 5000 steps with 192 atoms

Performance: 64.625 ns/day, 0.371 hours/ns, 249.324 timesteps/s, 47.870 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 10.926     | 10.926     | 10.926     |   0.0 | 54.48
Bond    | 0.033095   | 0.033095   | 0.033095   |   0.0 |  0.17
Kspace  | 3.0533     | 3.0533     | 3.0533     |   0.0 | 15.23
Neigh   | 3.4356     | 3.4356     | 3.4356     |   0.0 | 17.13
Comm    | 0.6031     | 0.6031     | 0.6031     |   0.0 |  3.01
Output  | 0.0011959  | 0.0011959  | 0.0011959  |   0.0 |  0.01
Modify  | 1.9814     | 1.9814     | 1.9814     |   0.0 |  9.88
Other   |            | 0.0204     |            |       |  0.10

Nlocal:            192 ave         192 max         192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6639 ave        6639 max        6639 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         115940 ave      115940 max      115940 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 115940
Ave neighs/atom = 603.85417
Ave special neighs/atom = 2
Neighbor list builds = 662
Dangerous builds = 0
Total wall time: 0:00:23
